GeneBe

rs776920005

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_000421.5(KRT10):​c.1683_1684insAGCTCCGGCGGCGGCTACGGCGGCGGCAGCAGCTCCGGCGGCGGATACGGCGGCGGCAGC​(p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySerSerSerGlyGlyGlyTyrGlyGlyGlySer) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 130,766 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000023 ( 1 hom., cov: 33)

Consequence

KRT10
NM_000421.5 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0440
Variant links:
Genes affected
KRT10 (HGNC:6413): (keratin 10) This gene encodes a member of the type I (acidic) cytokeratin family, which belongs to the superfamily of intermediate filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament. These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells. Mutations in this gene are associated with epidermolytic hyperkeratosis. This gene is located within a cluster of keratin family members on chromosome 17q21. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_000421.5.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KRT10NM_000421.5 linkc.1683_1684insAGCTCCGGCGGCGGCTACGGCGGCGGCAGCAGCTCCGGCGGCGGATACGGCGGCGGCAGC p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySerSerSerGlyGlyGlyTyrGlyGlyGlySer conservative_inframe_insertion Exon 7 of 8 ENST00000269576.6 NP_000412.4 P13645
KRT10NM_001379366.1 linkc.1683_1684insAGCTCCGGCGGCGGCTACGGCGGCGGCAGCAGCTCCGGCGGCGGATACGGCGGCGGCAGC p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySerSerSerGlyGlyGlyTyrGlyGlyGlySer conservative_inframe_insertion Exon 7 of 8 NP_001366295.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KRT10ENST00000269576.6 linkc.1683_1684insAGCTCCGGCGGCGGCTACGGCGGCGGCAGCAGCTCCGGCGGCGGATACGGCGGCGGCAGC p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySerSerSerGlyGlyGlyTyrGlyGlyGlySer conservative_inframe_insertion Exon 7 of 8 1 NM_000421.5 ENSP00000269576.5 P13645
KRT10ENST00000635956.2 linkc.1683_1684insAGCTCCGGCGGCGGCTACGGCGGCGGCAGCAGCTCCGGCGGCGGATACGGCGGCGGCAGC p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySerSerSerGlyGlyGlyTyrGlyGlyGlySer conservative_inframe_insertion Exon 7 of 8 2 ENSP00000490524.2 A0A1B0GVI3

Frequencies

GnomAD3 genomes
AF:
0.0000229
AC:
3
AN:
130766
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000308
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000325
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
AF:
0.0000229
AC:
3
AN:
130766
Hom.:
1
Cov.:
33
AF XY:
0.0000157
AC XY:
1
AN XY:
63586
show subpopulations
Gnomad4 AFR
AF:
0.0000308
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000325
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs776920005; hg19: chr17-38975103; API